Submissions from 2017
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, and Jing He
Efficient Core Utilization in a Hybrid Parallel Delaunay Meshing Algorithm on Distributed-Memory Cluster, Daming Feng, Andrey N. Chernikov, and Nikos P. Chrisochoides
Impact of URI Canonicalization on Memento Count, Mat Kelly, Lulwah M. Alkwai, Michael L. Nelson, Michele C. Weigle, and Herbert Van De Sompel
An Iterative Bézier Method for Fitting Beta-Sheet Component of a Cryo-EM Density Map, Michael Poteat and Jing He
ANSI/NISO Z39.99-2017 ResourceSync Framework Specification, Kevin Ruthen, Jill Emery, Mark Doyle, Mark Needleman, Sue Baughman, Evan Owens, Oliver Pesch, Mike Dicus, Nassib Nassar, Tim Auger, Amy Kirchhoff, Sally McCallum, Diana Magnoni, Paul Swanson, Gregory Grazevich, Nara Newcomer, Gregory Grazevich, Juha Hakala, Barbara Rapp, Beverly Geckle, Carol Brent, Gary Van Overborg, Rick Burke, Kristin Antelman, Scott Bernier, Pascal Calarco, John Dove, Lucy Harrison, Peter Murray, Christine Stohn, Julie Zhu, Todd Carpenter, Bernhard Haslhofer, Richard Jones, Martin Klein, Graham Klyne, Carl Lagoze, Stuart Lewis, Peter Murray, Michael Nelson, Shlomo Sanders, Robert Sanderson, Herbert Van de Sompel, Paul Walk, Simeon Warner, Zhiwu Xie, and Jeff Young
Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps, Dong Si and Jing He
Homeomorphic Tetrahedralization of Multi-material Images with Quality and Fidelity Guarantees, Jing Xu and Andrey N. Chernikov
Homeomorphic Tetrahedral Tessellation for Biomedical Images, Jing Xu and Andrey N. Chernikov
Comparing an Atomic Model or Structure to a Corresponding Cryo-Electron Microscopy Image at the Central Axis of a Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, and Jing He
Submissions from 2016
Leveraging Heritrix and the Wayback Machine on a Corporate Intranet: A Case Study on Improving Corporate Archives, Justin F. Brunelle, Krista Ferrante, Eliot Wilczek, Michele C. Weigle, and Michael L. Nelson
Deep Models for Brain EM Image Segmentation: Novel Insights and improved Performance, Ahmed Fakhry, Hanchuan Peng, and Shuiwang Ji
A Hybrid Parallel Delaunay Image-to-Mesh Conversion Algorithm Scalable on Distributed-memory Clusters, Daming Feng, Andrey N. Chernikov, and Nikos Chrisochoides
Mementos in the Raw, Shawn M. Jones, Herbert Van de Sompel, and Michael L. Nelson
Big Data-Enabled Multiscale Serviceability Analysis for Aging Bridges, Yu Liang, Dalei Wu, Guirong Liu, Yaohang Li, Cuilan Gao, Zhongguo John Ma, and Weidong Wu
A Hybrid Algorithm Based on Optimal Quadratic Spline Collocation and Parareal Deferred Correction for Parabolic PDEs, Jun Liu, Yan Wang, and Rongjian Li
RCD+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, and Pablo Chacón
Mementos in the Raw, Take Two, Herbert Van de Sompel, Michael L. Nelson, Lyudmila Balakireva, Martin Klein, Shawn M. Jones, and Harihar Shankar
FLEXc: Protein Flexibility Prediction Using Context-Based Statistics, Predicted Structural Features, and Sequence Information, Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, and Yaohang Li
Interactively Cutting and Constraining Vertices in Meshes Using Augmented Matrices, Yu-Hong Yeung, Jessica Crouch, and Alex Pothen
Submissions from 2015
Characteristics of Social Media Stories, Yasmin AINoamany, Michele C. Weigle, and Michael L. Nelson
Profiling Web Archives for Efficient Memento Query Routing, Sawood Alam, Michael L. Nelson, Herbert Van de Sompel, Lyudmila L. Balakireva, Harihar Shankar, and David S. H. Rosenthal
ISQuest: Finding Insertion Sequences in Prokaryotic Sequence Fragment Data, Abhishek Biswas, David T. Gauthier, Desh Ranjan, and Mohammad Zubair
A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, and Jing He
Extreme-Scale Parallel Mesh Generation: Telescopic Approach, Nikos Chrisochoides, Andrey Chernikov, Daming Feng, and Christos Tsolakis
Tetrahedral Image-to-Mesh Conversion Software for Anatomic Modeling of Arteriovenous Malformations, Fotis Drakopoulos, Ricardo Ortiz, Andinet Enquobahrie, Deanna Sasaki-Adams, and Nikos Chrisochoides
Global Analysis of Gene Expression and Projection Target Correlations in the Mouse Brain, Ahmed Fakhry, Tao Zeng, Hanchuan Peng, and Shuiwang Ji
Scalable 3D Hybrid Parallel Delaunay Image-to-Mesh Conversion Algorithm for Distributed Shared Memory Architectures, Daming Feng, Christos Tsolakis, Andrey N. Chernikov, and Nikos P. Chrisochoides
Making Sense of Video Analytics: Lessons Learned from Clickstream Interactions, Attitudes, and Learning Outcome in a Video-Assisted Course, Michail N. Giannakos, Konstantinos Chorianopoulos, and Nikos Chrisochoides
Scaffolding to Improve Writing Skills in a Computer Science Literacy Course, Wu He, Harris Wu, Li Xu, and Kurt Maly
Saccharomyces Boulardii and Bismuth Subsalicylate as Low-Cost Interventions to Reduce the Duration and Severity of Cholera, Johnathan Sheele, Jessica Cartowski, Angela Dart, Arjun Poddar, Shikha Gupta, and Ajay Gupta
High-Performance Simulations of Coherent Synchrotron Radiation on Multicore GPU and CPU Platforms, B. Terzić, A. Godunov, K. Arumugam, D. Ranjan, and M. Zubair
Reminiscing About 15 Years of Interoperability Efforts, Herbert Van de Sompel and Michael L. Nelson
Numerical Geometry of Map and Model Assessment, Willy Wriggers and Jing He
Deep Convolutional Neural Networks for Annotating Gene Expression Patterns in the Mouse Brain, Tao Zeng, Rongjian Li, Ravi Mukkamala, Jieping Ye, and Shuiwang Ji
Submissions from 2014
Toward a Real Time Multi-Tissue Adaptive Physics Based Non-Rigid Registration Framework for Brain Tumor Resection, Fotis Drakopoulos, Panagiotis Foteinos, Yixun Liu, and Nikos Chrisochoides
Moved But Not Gone: An Evaluation of Real-Time Methods for Discovering Replacement Web Pages, Martin Klein and Michael L. Nelson
Automated Identification of Cell Type Specific Genes in the Mouse Brain by Image Computing of Expression Patterns, Rongjian Li, Wenlu Zhang, and Shuiwang Ji
A Nonrigid Registration Method for Correcting Brain Deformation Induced by Tumor Resection, Yixun Liu, Chengjun Yao, Fotis Drakopoulos, Jinsong Wu, Liangfu Zhou, and Nikos Chrisochoides
A Scalable Backward Chaining-Based Reasoner for a Semantic Web, Hui Shi, Kurt Maly, and Steven Zeil
Tracing Beta Strands Using StrandTwister from Cryo-EM Density Maps at Medium Resolutions, Dong Si and Jing He
GPU Accelerated Long-Term Simulations of Beam-Beam Effects in Colliders, B. Terzić, V. Morozov, Y. Roblin, F. Lin, H. Zhang, M. Aturban, D. Ranjan, and M. Zubair
Automatic Curvilinear Quality Mesh Generation Driven by Smooth Boundary and Guaranteed Fidelity, Jing Xu and Andrey N. Chernikov
Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information and Context-Based Features, Ashraf Yaseen and Yaohang Li
Submissions from 2013
The 6th Computational Structural Bioinformatics Workshop Introduction, Jing He, Amarda Shehu, Nurit Haspel, and Brian Chen
Convergence Analysis of Markov Chain Monte Carlo Linear Solvers Using Ulam--von Neumann Algorithm, Hao Ji, Michael Mascagni, and Yaohang Li
A Method for Identifying Personalized Representations in Web Archives, Mat Kelly, Justin F. Brunelle, Michele C. Weigle, and Michael L. Nelson
WARCreate and WAIL: WARC, Wayback, and Heritrix Made Easy, Mat Kelly, Michael L. Nelson, and Michele C. Weigle
A Technical Framework for Resource Synchronization, Martin Klein, Robert Sanderson, Herbert Van de Sompel, Simeon Warner, Bernhard Haslhofer, Carl Lagoze, and Michael L. Nelson
Conformational Sampling in Template Free Protein Loop Structure Modeling: An Overview, Yaohang Li
Estimating Loop Length from CryoEM Images at Medium Resolutions, Andrew McKnight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, and Jing He
Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, and Jing He
Game Walkthroughs as a Metaphor for Web Preservation, Michael L. Nelson
Wayback Machine Upgrades Memento Support, Michael L. Nelson
GPU-optimized Code for Long-term Simulations of Beam-beam Effects in Colliders, Y. Roblin, V. Morozov, B. Terzić, M. Aturban, D. Ranjan, and M. Zubair
Image-Level and Group-Level Models for Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, and Jieping Ye
Thoughts on Referencing, Linking, Reference Rot, Herbert Van de Sompel, Martin Klein, Robert Sanderson, and Michael Nelson
HTTP Framework for Time-Based Access to Resource States - Memento, Herbert Van de Sompel, Michael L. Nelson, and Robert Sanderson
Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features to Enhance Prediction Accuracy, Ashraf Yaseen and Yaohang Li
A Mesh Generation and Machine Learning Framework for Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, and Shuiwang Ji
Submissions from 2012
On a Versatile Stochastic Growth Model, Samiur Arif, Ismail Khalil, and Stephan Olariu
Generalized Insertion Region Guides for Delaunay Mesh Refinement, Andrey Chernikov and Nikos Chrisochoides
WARCreate: Create Wayback-Consumable WARC Files From Any Webpage, Mat Kelly and Michele C. Weigle
WARCreate - Create Wayback-Consumable WARC Files From Any Webpage, Mat Kelly, Michele C. Weigle, and Michael L. Nelson
MOMCMC: An Efficient Monte Carlo Method for Multi-Objective Sampling Over Real Parameter Space, Yaohang Li
Demographic Prediction of Mobile User from Phone Usage, Shahram Mohrehkesh, Shuiwang Ji, Tamer Nadeem, and Michele C. Weigle
Cooperation as a Service in VANET: Implementation and Simulation Results, Hajar Mousannif, Ismail Khalil, and Stephan Olariu
A Perspective on Resource Synchronization, Herbert Van de Sompel, Robert Sanderson, Martin Klein, Michael L. Nelson, Bernhard Haslhofer, Simeon Warner, and Carl Lagoze
Learning Sparse Representations for Fruit Fly Gene Expression Pattern Image Annotation and Retreival, Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar, and Jieping Ye
Submissions from 2011
Special Issue on Wireless Sensor and Actuator Networks, Jiming Chen, Karl H. Johanson, Stephan Olariu, Ioannis Ch. Paschalidis, and Ivan Stojmenovic
Multitissue Tetrahedral Image-to-Mesh Conversion with Guaranteed Quality and Fidelity, Andrey N. Chernikov and Nikos P. Chrisochoides
User Experiments of a Social, Faceted Multimedia Classification System, LiuLiu Fu, Kurt Maly, Elizabeth Rasnick, Harris Wu, and Mohammad Zubair
Computational Network Analysis of the Anatomical and Genetic Organizations in the Mouse Brain, Shuiwang Ji
Vehicular Ad Hoc Networks, Syed R. Rizvi, Stephan Olariu, Christina M. Oinotti, Shaharuddin Salleh, Mona E. Rizvi, and Zainab Zaidi
From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation, Weitao Sun and Jing He
Submissions from 2010
Fully Generalized Two-Dimensional Constrained Delaunay Mesh Refinement, Panagiotis A. Foteinos, Andrey N. Chernikov, and Nikos P. Chrisochoides
The 3rd Computational Structural Bioinformatics Workshop, Jing He and Di Wu
Improving Predicted Protein Loop Structure Ranking Using a Pareto-Optimality Consensus Method, Yaohang Li, Ionel Rata, See-Wing Chiu, and Erik Jakobsson
Structure Prediction for the Helical Skeletons Detected from the Low Resolution Protein Density Map, Kamal Al Nasr, Weitao Sun, and Jing He
Memento-Datetime is Not Last-Modified, Michael L. Nelson
Submissions from 2009
Multicast Encryption Infrastructure for Security in Sensor Networks, Richard R. Brooks, Brijesh Pillai, Matthew Pirretti, and Michele C. Weigle
Correlation of Music Charts and Search Engine Rankings, Martin Klein, Olena Hunsicker, and Michael Nelson
Everyone is a Curator: Human-Assisted Preservation for ORE Aggregations, Frank McCown, Michael L. Nelson, and Herbert Van de Sompel
Object Reuse and Exchange, Michael L. Nelson, Carl Lagoze, Herbert Van de Sompel, Pete Johnston, Robert Sanderson, Simeon Warner, Jürgen Sieck (Ed.), and Michael A. Herzog (Ed.)
Dynamic Adaptation of Joint Transmission Power and Contention Window in VANET, Danda B. Rawat, Gongjun Yan, Dimitrie C. Popescu, Michele C. Weigle, and Stephan Olariu
Evaluating Multicore Algorithms on the Unified Memory Model, John E. Savage and Mohammad Zubair
Adding eScience Assets to the Data Web, Herbert H. Van de Sompel, Carl Lagoze, Michael L. Nelson, Simeon Warner, Robert Sanderson, and Pete Johnston
Submissions from 2008
Efficient Corona Training Protocols for Sensor Networks, Alan A. Bertossi, Stephan Olariu, and Cristina M. Pinotti
Dedication to Pierre Lallemand on the Occasion of His Retirement, Dominque d'Humieres, Manfred Krafczyk, Li-Shi Luo, and Robert Rubinstein
Emergent Behavior in Massively-Deployed Sensor Networks, Ekaterina Shurkova, Ruzana Ishak, Stephan Olariu, and Shaharuddin Salleh
Creating Preservation-Ready Web Resources, Joan A. Smith and Michael L. Nelson
Submissions from 2007
Optimal Layout of Multicast Groups Using Network Embedded Multicast Security in Ad Hoc Sensor Networks, Richard R. Brooks, Brijesh Pillai, Michele C. Weigle, and Matthew Pirretti
All Minimal Prime Extensions of Hereditary Classes of Graphs, Vassilis Giakoumakis and Stephan Olariu
Assessing the Format of the Presentation of Text in Developing a Reading Strategy Assessment Tool (R-SAT), Sara Gilliam, Joseph P. Magliano, Keith K. Millis, Irwin Levinstein, and Chutima Boonthum
Hybrid Training With Binary Search Protocol for Wireless Sensor Networks, Ruzana Ishak, Qingwen Xu, Stephan Olariu, and Shaharuddin Salleh
How Much Preservation Do I Get if I Do Absolutely Nothing? Using the Web Infrastructure for Digital Preservation, Martin Klein, Frank McCown, Joan A. Smith, and Michael Nelson
iSTART 2: Improvements for Efficiency and Effectiveness, Irwin B. Levinstein, Chutima Boonthum, Srinivasa P. Pillarisetti, Courtney Bell, and Danielle S. McNamara
Brass: A Queueing Manager for Warrick, Frank McCown, Amine Benjelloun, and Michael L. Nelson
Factors Affecting Website Reconstruction From the Web Infrastructure, Frank McCown, Norou Diawara, and Michael L. Nelson
CRATE: A Simple Model for Self-Describing Web Resources, Joan A. Smith and Michael L. Nelson